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value | code stringlengths 73 34.1k | code_tokens list | docstring stringlengths 3 16k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 105 339 |
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500 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionManager.java | TransactionManager.startMetricsThread | private void startMetricsThread() {
LOG.info("Starting periodic Metrics Emitter thread, frequency = " + METRICS_POLL_INTERVAL);
this.metricsThread = new DaemonThreadExecutor("tx-metrics") {
@Override
public void doRun() {
txMetricsCollector.gauge("committing.size", committingChangeSets.size(... | java | private void startMetricsThread() {
LOG.info("Starting periodic Metrics Emitter thread, frequency = " + METRICS_POLL_INTERVAL);
this.metricsThread = new DaemonThreadExecutor("tx-metrics") {
@Override
public void doRun() {
txMetricsCollector.gauge("committing.size", committingChangeSets.size(... | [
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501 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionManager.java | TransactionManager.takeSnapshot | public boolean takeSnapshot(OutputStream out) throws IOException {
TransactionSnapshot snapshot = getSnapshot();
if (snapshot != null) {
persistor.writeSnapshot(out, snapshot);
return true;
} else {
return false;
}
} | java | public boolean takeSnapshot(OutputStream out) throws IOException {
TransactionSnapshot snapshot = getSnapshot();
if (snapshot != null) {
persistor.writeSnapshot(out, snapshot);
return true;
} else {
return false;
}
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502 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionManager.java | TransactionManager.restoreSnapshot | private void restoreSnapshot(TransactionSnapshot snapshot) {
LOG.info("Restoring transaction state from snapshot at " + snapshot.getTimestamp());
Preconditions.checkState(lastSnapshotTime == 0, "lastSnapshotTime has been set!");
Preconditions.checkState(readPointer == 0, "readPointer has been set!");
Pr... | java | private void restoreSnapshot(TransactionSnapshot snapshot) {
LOG.info("Restoring transaction state from snapshot at " + snapshot.getTimestamp());
Preconditions.checkState(lastSnapshotTime == 0, "lastSnapshotTime has been set!");
Preconditions.checkState(readPointer == 0, "readPointer has been set!");
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503 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionManager.java | TransactionManager.txnBackwardsCompatCheck | public static Map<Long, InProgressTx> txnBackwardsCompatCheck(int defaultLongTimeout, long longTimeoutTolerance,
Map<Long, InProgressTx> inProgress) {
for (Map.Entry<Long, InProgressTx> entry : inProgress.entrySet()) {
long writePointer = entry.g... | java | public static Map<Long, InProgressTx> txnBackwardsCompatCheck(int defaultLongTimeout, long longTimeoutTolerance,
Map<Long, InProgressTx> inProgress) {
for (Map.Entry<Long, InProgressTx> entry : inProgress.entrySet()) {
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504 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionManager.java | TransactionManager.resetState | public void resetState() {
this.logWriteLock.lock();
try {
// Take a snapshot before resetting the state, for debugging purposes
doSnapshot(false);
// Clear the state
clear();
// Take another snapshot: if no snapshot is taken after clearing the state
// and the manager is res... | java | public void resetState() {
this.logWriteLock.lock();
try {
// Take a snapshot before resetting the state, for debugging purposes
doSnapshot(false);
// Clear the state
clear();
// Take another snapshot: if no snapshot is taken after clearing the state
// and the manager is res... | [
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505 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionManager.java | TransactionManager.abortService | private void abortService(String message, Throwable error) {
if (isRunning()) {
LOG.error("Aborting transaction manager due to: " + message, error);
notifyFailed(error);
}
} | java | private void abortService(String message, Throwable error) {
if (isRunning()) {
LOG.error("Aborting transaction manager due to: " + message, error);
notifyFailed(error);
}
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506 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionManager.java | TransactionManager.startShort | public Transaction startShort(int timeoutInSeconds) {
Preconditions.checkArgument(timeoutInSeconds > 0, "timeout must be positive but is %s", timeoutInSeconds);
txMetricsCollector.rate("start.short");
Stopwatch timer = new Stopwatch().start();
long expiration = getTxExpiration(timeoutInSeconds);
Tra... | java | public Transaction startShort(int timeoutInSeconds) {
Preconditions.checkArgument(timeoutInSeconds > 0, "timeout must be positive but is %s", timeoutInSeconds);
txMetricsCollector.rate("start.short");
Stopwatch timer = new Stopwatch().start();
long expiration = getTxExpiration(timeoutInSeconds);
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507 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionManager.java | TransactionManager.startLong | public Transaction startLong() {
txMetricsCollector.rate("start.long");
Stopwatch timer = new Stopwatch().start();
long expiration = getTxExpiration(defaultLongTimeout);
Transaction tx = startTx(expiration, TransactionType.LONG);
txMetricsCollector.histogram("start.long.latency", (int) timer.elapsed... | java | public Transaction startLong() {
txMetricsCollector.rate("start.long");
Stopwatch timer = new Stopwatch().start();
long expiration = getTxExpiration(defaultLongTimeout);
Transaction tx = startTx(expiration, TransactionType.LONG);
txMetricsCollector.histogram("start.long.latency", (int) timer.elapsed... | [
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508 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionManager.java | TransactionManager.truncateInvalidTx | public boolean truncateInvalidTx(Set<Long> invalidTxIds) {
// guard against changes to the transaction log while processing
txMetricsCollector.rate("truncateInvalidTx");
Stopwatch timer = new Stopwatch().start();
this.logReadLock.lock();
try {
boolean success;
synchronized (this) {
... | java | public boolean truncateInvalidTx(Set<Long> invalidTxIds) {
// guard against changes to the transaction log while processing
txMetricsCollector.rate("truncateInvalidTx");
Stopwatch timer = new Stopwatch().start();
this.logReadLock.lock();
try {
boolean success;
synchronized (this) {
... | [
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509 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionManager.java | TransactionManager.truncateInvalidTxBefore | public boolean truncateInvalidTxBefore(long time) throws InvalidTruncateTimeException {
// guard against changes to the transaction log while processing
txMetricsCollector.rate("truncateInvalidTxBefore");
Stopwatch timer = new Stopwatch().start();
this.logReadLock.lock();
try {
boolean success... | java | public boolean truncateInvalidTxBefore(long time) throws InvalidTruncateTimeException {
// guard against changes to the transaction log while processing
txMetricsCollector.rate("truncateInvalidTxBefore");
Stopwatch timer = new Stopwatch().start();
this.logReadLock.lock();
try {
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510 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionManager.java | TransactionManager.createTransaction | private Transaction createTransaction(long writePointer, TransactionType type) {
// For holding the first in progress short transaction Id (with timeout >= 0).
long firstShortTx = Transaction.NO_TX_IN_PROGRESS;
LongArrayList inProgressIds = new LongArrayList(inProgress.size());
for (Map.Entry<Long, InPr... | java | private Transaction createTransaction(long writePointer, TransactionType type) {
// For holding the first in progress short transaction Id (with timeout >= 0).
long firstShortTx = Transaction.NO_TX_IN_PROGRESS;
LongArrayList inProgressIds = new LongArrayList(inProgress.size());
for (Map.Entry<Long, InPr... | [
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511 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionManager.java | TransactionManager.logStatistics | public void logStatistics() {
LOG.info("Transaction Statistics: write pointer = " + lastWritePointer +
", invalid = " + invalid.size() +
", in progress = " + inProgress.size() +
", committing = " + committingChangeSets.size() +
", committed = " + committed... | java | public void logStatistics() {
LOG.info("Transaction Statistics: write pointer = " + lastWritePointer +
", invalid = " + invalid.size() +
", in progress = " + inProgress.size() +
", committing = " + committingChangeSets.size() +
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512 | cdapio/tephra | tephra-examples/src/main/java/co/cask/tephra/examples/BalanceBooks.java | BalanceBooks.init | public void init() throws IOException {
Injector injector = Guice.createInjector(
new ConfigModule(conf),
new ZKModule(),
new DiscoveryModules().getDistributedModules(),
new TransactionModules().getDistributedModules(),
new TransactionClientModule()
);
zkClient = inj... | java | public void init() throws IOException {
Injector injector = Guice.createInjector(
new ConfigModule(conf),
new ZKModule(),
new DiscoveryModules().getDistributedModules(),
new TransactionModules().getDistributedModules(),
new TransactionClientModule()
);
zkClient = inj... | [
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513 | cdapio/tephra | tephra-examples/src/main/java/co/cask/tephra/examples/BalanceBooks.java | BalanceBooks.run | public void run() throws IOException, InterruptedException {
List<Client> clients = new ArrayList<>(totalClients);
for (int i = 0; i < totalClients; i++) {
Client c = new Client(i, totalClients, iterations);
c.init(txClient, conn.getTable(TABLE));
c.start();
clients.add(c);
}
fo... | java | public void run() throws IOException, InterruptedException {
List<Client> clients = new ArrayList<>(totalClients);
for (int i = 0; i < totalClients; i++) {
Client c = new Client(i, totalClients, iterations);
c.init(txClient, conn.getTable(TABLE));
c.start();
clients.add(c);
}
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514 | cdapio/tephra | tephra-examples/src/main/java/co/cask/tephra/examples/BalanceBooks.java | BalanceBooks.close | public void close() {
try {
if (conn != null) {
conn.close();
}
} catch (IOException ignored) { }
if (zkClient != null) {
zkClient.stopAndWait();
}
} | java | public void close() {
try {
if (conn != null) {
conn.close();
}
} catch (IOException ignored) { }
if (zkClient != null) {
zkClient.stopAndWait();
}
} | [
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515 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/snapshot/BinaryDecoder.java | BinaryDecoder.readBytes | public byte[] readBytes() throws IOException {
int toRead = readInt();
byte[] bytes = new byte[toRead];
while (toRead > 0) {
int byteRead = input.read(bytes, bytes.length - toRead, toRead);
if (byteRead == -1) {
throw new EOFException();
}
toRead -= byteRead;
}
return... | java | public byte[] readBytes() throws IOException {
int toRead = readInt();
byte[] bytes = new byte[toRead];
while (toRead > 0) {
int byteRead = input.read(bytes, bytes.length - toRead, toRead);
if (byteRead == -1) {
throw new EOFException();
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516 | cdapio/tephra | tephra-core/src/main/java/org/apache/thrift/server/TThreadedSelectorServerWithFix.java | TThreadedSelectorServerWithFix.startThreads | @Override
protected boolean startThreads() {
LOGGER.info("Starting {}", TThreadedSelectorServerWithFix.class.getSimpleName());
try {
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selectorThreads.add(new SelectorThread(args.acceptQueueSizePerThread));
}
acceptThread = new AcceptThr... | java | @Override
protected boolean startThreads() {
LOGGER.info("Starting {}", TThreadedSelectorServerWithFix.class.getSimpleName());
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selectorThreads.add(new SelectorThread(args.acceptQueueSizePerThread));
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517 | cdapio/tephra | tephra-core/src/main/java/org/apache/thrift/server/TThreadedSelectorServerWithFix.java | TThreadedSelectorServerWithFix.stop | @Override
public void stop() {
stopped_ = true;
// Stop queuing connect attempts asap
stopListening();
if (acceptThread != null) {
acceptThread.wakeupSelector();
}
if (selectorThreads != null) {
for (SelectorThread thread : selectorThreads) {
if (thread != null)
... | java | @Override
public void stop() {
stopped_ = true;
// Stop queuing connect attempts asap
stopListening();
if (acceptThread != null) {
acceptThread.wakeupSelector();
}
if (selectorThreads != null) {
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518 | cdapio/tephra | tephra-core/src/main/java/org/apache/thrift/server/TThreadedSelectorServerWithFix.java | TThreadedSelectorServerWithFix.requestInvoke | @Override
protected boolean requestInvoke(FrameBuffer frameBuffer) {
Runnable invocation = getRunnable(frameBuffer);
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try {
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return true;
} catch (RejectedExecutionException rx) {
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Runnable invocation = getRunnable(frameBuffer);
if (invoker != null) {
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invoker.execute(invocation);
return true;
} catch (RejectedExecutionException rx) {
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519 | cdapio/tephra | tephra-core/src/main/java/org/apache/thrift/server/TThreadedSelectorServerWithFix.java | TThreadedSelectorServerWithFix.createDefaultExecutor | protected static ExecutorService createDefaultExecutor(Args options) {
return (options.workerThreads > 0) ? Executors.newFixedThreadPool(options.workerThreads) : null;
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520 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/snapshot/BinaryEncoder.java | BinaryEncoder.writeInt | public BinaryEncoder writeInt(int i) throws IOException {
// Compute the zig-zag value. First double the value and flip the bit if the input is negative.
int val = (i << 1) ^ (i >> 31);
if ((val & ~0x7f) != 0) {
output.write(0x80 | val & 0x7f);
val >>>= 7;
while (val > 0x7f) {
out... | java | public BinaryEncoder writeInt(int i) throws IOException {
// Compute the zig-zag value. First double the value and flip the bit if the input is negative.
int val = (i << 1) ^ (i >> 31);
if ((val & ~0x7f) != 0) {
output.write(0x80 | val & 0x7f);
val >>>= 7;
while (val > 0x7f) {
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521 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/snapshot/BinaryEncoder.java | BinaryEncoder.writeLong | public BinaryEncoder writeLong(long l) throws IOException {
// Compute the zig-zag value. First double the value and flip the bit if the input is negative.
long val = (l << 1) ^ (l >> 63);
if ((val & ~0x7f) != 0) {
output.write((int) (0x80 | val & 0x7f));
val >>>= 7;
while (val > 0x7f) {
... | java | public BinaryEncoder writeLong(long l) throws IOException {
// Compute the zig-zag value. First double the value and flip the bit if the input is negative.
long val = (l << 1) ^ (l >> 63);
if ((val & ~0x7f) != 0) {
output.write((int) (0x80 | val & 0x7f));
val >>>= 7;
while (val > 0x7f) {
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522 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/snapshot/BinaryEncoder.java | BinaryEncoder.writeBytes | public BinaryEncoder writeBytes(byte[] bytes) throws IOException {
writeLong(bytes.length);
output.write(bytes, 0, bytes.length);
return this;
} | java | public BinaryEncoder writeBytes(byte[] bytes) throws IOException {
writeLong(bytes.length);
output.write(bytes, 0, bytes.length);
return this;
} | [
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523 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/persist/CommitMarkerCodec.java | CommitMarkerCodec.readMarker | public int readMarker(SequenceFile.Reader reader) throws IOException {
if (valueBytes == null) {
valueBytes = reader.createValueBytes();
}
rawKey.reset();
rawValue.reset();
// valueBytes need not be reset since nextRaw call does it (and it is a private method)
int status = reader.nextRaw(... | java | public int readMarker(SequenceFile.Reader reader) throws IOException {
if (valueBytes == null) {
valueBytes = reader.createValueBytes();
}
rawKey.reset();
rawValue.reset();
// valueBytes need not be reset since nextRaw call does it (and it is a private method)
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524 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/coprocessor/TransactionStateCache.java | TransactionStateCache.tryInit | private void tryInit() {
try {
Configuration conf = getSnapshotConfiguration();
if (conf != null) {
// Since this is only used for background loading of transaction snapshots, we use the no-op metrics collector,
// as there are no relevant metrics to report
this.storage = new HDF... | java | private void tryInit() {
try {
Configuration conf = getSnapshotConfiguration();
if (conf != null) {
// Since this is only used for background loading of transaction snapshots, we use the no-op metrics collector,
// as there are no relevant metrics to report
this.storage = new HDF... | [
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525 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionServiceMain.java | TransactionServiceMain.doMain | public void doMain(final String[] args) throws Exception {
final CountDownLatch shutdownLatch = new CountDownLatch(1);
Runtime.getRuntime().addShutdownHook(new Thread() {
@Override
public void run() {
try {
try {
TransactionServiceMain.this.stop();
} finally {
... | java | public void doMain(final String[] args) throws Exception {
final CountDownLatch shutdownLatch = new CountDownLatch(1);
Runtime.getRuntime().addShutdownHook(new Thread() {
@Override
public void run() {
try {
try {
TransactionServiceMain.this.stop();
} finally {
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526 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionServiceMain.java | TransactionServiceMain.start | public void start() throws Exception {
Injector injector = Guice.createInjector(
new ConfigModule(conf),
new ZKModule(),
new DiscoveryModules().getDistributedModules(),
new TransactionModules().getDistributedModules(),
new TransactionClientModule()
);
ZKClientService zkClientS... | java | public void start() throws Exception {
Injector injector = Guice.createInjector(
new ConfigModule(conf),
new ZKModule(),
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new TransactionModules().getDistributedModules(),
new TransactionClientModule()
);
ZKClientService zkClientS... | [
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527 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/TransactionServiceMain.java | TransactionServiceMain.stop | public void stop() {
LOG.info("Stopping {}", getClass().getSimpleName());
if (txService == null) {
return;
}
try {
if (txService.isRunning()) {
txService.stopAndWait();
}
} catch (Throwable e) {
LOG.error("Failed to shutdown transaction service.", e);
// because... | java | public void stop() {
LOG.info("Stopping {}", getClass().getSimpleName());
if (txService == null) {
return;
}
try {
if (txService.isRunning()) {
txService.stopAndWait();
}
} catch (Throwable e) {
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528 | cdapio/tephra | tephra-core/src/main/java/co/cask/tephra/distributed/ElasticPool.java | ElasticPool.getOrCreate | private T getOrCreate() throws E {
try {
T client = elements.poll();
// a client was available, all good. otherwise, create one
if (client != null) {
return client;
}
return create();
} catch (Exception e) {
// if an exception is thrown after acquiring the semaphore, ... | java | private T getOrCreate() throws E {
try {
T client = elements.poll();
// a client was available, all good. otherwise, create one
if (client != null) {
return client;
}
return create();
} catch (Exception e) {
// if an exception is thrown after acquiring the semaphore, ... | [
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529 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/Skew.java | Skew.leq | private static boolean leq(int a1, int a2, int b1, int b2) {
return (a1 < b1 || (a1 == b1 && a2 <= b2));
} | java | private static boolean leq(int a1, int a2, int b1, int b2) {
return (a1 < b1 || (a1 == b1 && a2 <= b2));
} | [
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530 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/Skew.java | Skew.leq | private static boolean leq(int a1, int a2, int a3, int b1, int b2, int b3) {
return (a1 < b1 || (a1 == b1 && leq(a2, a3, b2, b3)));
} | java | private static boolean leq(int a1, int a2, int a3, int b1, int b2, int b3) {
return (a1 < b1 || (a1 == b1 && leq(a2, a3, b2, b3)));
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531 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/BPR.java | BPR.insSortUpdateRecurse_SaBucket | private void insSortUpdateRecurse_SaBucket(int leftPtr, int rightPtr, int offset,
int q) {
int rightTmpPtr = leftPtr + 1;
while (rightTmpPtr <= rightPtr) {
int tempValue = suffixArray[rightTmpPtr];
int tempHashValue = sufPtrMap[suffi... | java | private void insSortUpdateRecurse_SaBucket(int leftPtr, int rightPtr, int offset,
int q) {
int rightTmpPtr = leftPtr + 1;
while (rightTmpPtr <= rightPtr) {
int tempValue = suffixArray[rightTmpPtr];
int tempHashValue = sufPtrMap[suffi... | [
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@param leftPtr points to the leftmost suffix of the current bucket.
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@param offset is the length of the common prefix of the suffixe... | [
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532 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/BPR.java | BPR.computeBucketSize2_SaBucket | private void computeBucketSize2_SaBucket(int leftPtr, int rightPtr, int offset, int q) {
int suffix1 = suffixArray[leftPtr] + offset;
int suffix2 = suffixArray[rightPtr] + offset;
while (sufPtrMap[suffix1] == sufPtrMap[suffix2]) {
suffix1 += q;
suffix2 += q;
}
... | java | private void computeBucketSize2_SaBucket(int leftPtr, int rightPtr, int offset, int q) {
int suffix1 = suffixArray[leftPtr] + offset;
int suffix2 = suffixArray[rightPtr] + offset;
while (sufPtrMap[suffix1] == sufPtrMap[suffix2]) {
suffix1 += q;
suffix2 += q;
}
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533 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/BPR.java | BPR.computeDiffDepthBucket_SaBucket | private int computeDiffDepthBucket_SaBucket(int leftPtr, int rightPtr, int offset,
int q) {
int lcp = offset;
while (true) {
int runPtr = leftPtr;
int a = suffixArray[rightPtr];
int tmpPtr = sufPtrMap[a + lcp];
... | java | private int computeDiffDepthBucket_SaBucket(int leftPtr, int rightPtr, int offset,
int q) {
int lcp = offset;
while (true) {
int runPtr = leftPtr;
int a = suffixArray[rightPtr];
int tmpPtr = sufPtrMap[a + lcp];
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534 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/BPR.java | BPR.determineAll_Buckets_Sarray_Sptrmap | private int[] determineAll_Buckets_Sarray_Sptrmap(int q) {
int[] buckets = determineAll_Buckets_Sarray(q);
int strLen = length;
sufPtrMap = new int[strLen + 2 * q + 1];
/* computation of first hashvalue */
int alphabetSize = alphabet.size;
int mappedUcharArray = 0;
... | java | private int[] determineAll_Buckets_Sarray_Sptrmap(int q) {
int[] buckets = determineAll_Buckets_Sarray(q);
int strLen = length;
sufPtrMap = new int[strLen + 2 * q + 1];
/* computation of first hashvalue */
int alphabetSize = alphabet.size;
int mappedUcharArray = 0;
... | [
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535 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/BPR.java | BPR.determinePower2Alpha_Buckets_Sarray_Sptrmap | private int[] determinePower2Alpha_Buckets_Sarray_Sptrmap(int q) {
int strLen = length;
int exp2 = kbs_getExp_Ulong(2, alphabet.size);
if (exp2 < 0) {
throw new RuntimeException("value out of bounds");
}
int[] buckets = determinePower2Alpha_Buckets_Sarray(q);
... | java | private int[] determinePower2Alpha_Buckets_Sarray_Sptrmap(int q) {
int strLen = length;
int exp2 = kbs_getExp_Ulong(2, alphabet.size);
if (exp2 < 0) {
throw new RuntimeException("value out of bounds");
}
int[] buckets = determinePower2Alpha_Buckets_Sarray(q);
... | [
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536 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/DivSufSort.java | DivSufSort.ssMergeForward | private void ssMergeForward(int PA, int first, int middle, int last, int buf,
int depth) {
// PA, first, middle, last, buf are pointers to SA
int a, b, c, bufend;// pointers to SA
int t, r;
bufend = buf + (middle - first) - 1;
ssBlockSwap(buf, fir... | java | private void ssMergeForward(int PA, int first, int middle, int last, int buf,
int depth) {
// PA, first, middle, last, buf are pointers to SA
int a, b, c, bufend;// pointers to SA
int t, r;
bufend = buf + (middle - first) - 1;
ssBlockSwap(buf, fir... | [
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537 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/DivSufSort.java | DivSufSort.ssInsertionSort | private void ssInsertionSort(int PA, int first, int last, int depth) {
// PA, first, last are pointers in SA
int i, j;// pointers in SA
int t, r;
for (i = last - 2; first <= i; --i) {
for (t = SA[i], j = i + 1; 0 < (r = ssCompare(PA + t, PA + SA[j], depth)); ) {
... | java | private void ssInsertionSort(int PA, int first, int last, int depth) {
// PA, first, last are pointers in SA
int i, j;// pointers in SA
int t, r;
for (i = last - 2; first <= i; --i) {
for (t = SA[i], j = i + 1; 0 < (r = ssCompare(PA + t, PA + SA[j], depth)); ) {
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538 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/DivSufSort.java | DivSufSort.ssMedian5 | private int ssMedian5(int Td, int PA, int v1, int v2, int v3, int v4, int v5) {
int t;
if (T[start + Td + SA[PA + SA[v2]]] > T[start + Td + SA[PA + SA[v3]]]) {
t = v2;
v2 = v3;
v3 = t;
}
if (T[start + Td + SA[PA + SA[v4]]] > T[start + Td + SA[PA + SA[... | java | private int ssMedian5(int Td, int PA, int v1, int v2, int v3, int v4, int v5) {
int t;
if (T[start + Td + SA[PA + SA[v2]]] > T[start + Td + SA[PA + SA[v3]]]) {
t = v2;
v2 = v3;
v3 = t;
}
if (T[start + Td + SA[PA + SA[v4]]] > T[start + Td + SA[PA + SA[... | [
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539 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/DivSufSort.java | DivSufSort.ssPartition | private int ssPartition(int PA, int first, int last, int depth) {
int a, b;// SA pointer
int t;
for (a = first - 1, b = last; ; ) {
for (; (++a < b) && ((SA[PA + SA[a]] + depth) >= (SA[PA + SA[a] + 1] + 1)); ) {
SA[a] = ~SA[a];
}
for (; (a < --... | java | private int ssPartition(int PA, int first, int last, int depth) {
int a, b;// SA pointer
int t;
for (a = first - 1, b = last; ; ) {
for (; (++a < b) && ((SA[PA + SA[a]] + depth) >= (SA[PA + SA[a] + 1] + 1)); ) {
SA[a] = ~SA[a];
}
for (; (a < --... | [
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540 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/DivSufSort.java | DivSufSort.ssHeapSort | private void ssHeapSort(int Td, int PA, int sa, int size) {
int i, m, t;
m = size;
if ((size % 2) == 0) {
m--;
if (T[start + Td + SA[PA + SA[sa + (m / 2)]]] < T[start + Td
+ SA[PA + SA[sa + m]]]) {
swapInSA(sa + m, sa + (m / 2));
... | java | private void ssHeapSort(int Td, int PA, int sa, int size) {
int i, m, t;
m = size;
if ((size % 2) == 0) {
m--;
if (T[start + Td + SA[PA + SA[sa + (m / 2)]]] < T[start + Td
+ SA[PA + SA[sa + m]]]) {
swapInSA(sa + m, sa + (m / 2));
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541 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/DivSufSort.java | DivSufSort.trSort | private void trSort(int ISA, int n, int depth) {
TRBudget budget = new TRBudget(trIlg(n) * 2 / 3, n);
int ISAd;
int first, last;// SA pointers
int t, skip, unsorted;
for (ISAd = ISA + depth; -n < SA[0]; ISAd += ISAd - ISA) {
first = 0;
skip = 0;
... | java | private void trSort(int ISA, int n, int depth) {
TRBudget budget = new TRBudget(trIlg(n) * 2 / 3, n);
int ISAd;
int first, last;// SA pointers
int t, skip, unsorted;
for (ISAd = ISA + depth; -n < SA[0]; ISAd += ISAd - ISA) {
first = 0;
skip = 0;
... | [
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] | 76dd1fcc36047bc66a87d31142e72e98b5347821 | https://github.com/interedition/collatex/blob/76dd1fcc36047bc66a87d31142e72e98b5347821/collatex-core/src/main/java/eu/interedition/collatex/suffixarray/DivSufSort.java#L1378-L1419 |
542 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/DivSufSort.java | DivSufSort.trMedian5 | private int trMedian5(int ISAd, int v1, int v2, int v3, int v4, int v5) {
int t;
if (SA[ISAd + SA[v2]] > SA[ISAd + SA[v3]]) {
t = v2;
v2 = v3;
v3 = t;
}
if (SA[ISAd + SA[v4]] > SA[ISAd + SA[v5]]) {
t = v4;
v4 = v5;
v... | java | private int trMedian5(int ISAd, int v1, int v2, int v3, int v4, int v5) {
int t;
if (SA[ISAd + SA[v2]] > SA[ISAd + SA[v3]]) {
t = v2;
v2 = v3;
v3 = t;
}
if (SA[ISAd + SA[v4]] > SA[ISAd + SA[v5]]) {
t = v4;
v4 = v5;
v... | [
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543 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/DivSufSort.java | DivSufSort.trCopy | private void trCopy(int ISA, int first, int a, int b, int last, int depth) {
int c, d, e;// ptr
int s, v;
v = b - 1;
for (c = first, d = a - 1; c <= d; ++c) {
s = SA[c] - depth;
if ((0 <= s) && (SA[ISA + s] == v)) {
SA[++d] = s;
SA... | java | private void trCopy(int ISA, int first, int a, int b, int last, int depth) {
int c, d, e;// ptr
int s, v;
v = b - 1;
for (c = first, d = a - 1; c <= d; ++c) {
s = SA[c] - depth;
if ((0 <= s) && (SA[ISA + s] == v)) {
SA[++d] = s;
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544 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/Sequence.java | Sequence.add | void add(S sequence) {
for (I item : sequence) {
masterSequence.add(item);
}
SequenceTerminal<S> terminal = new SequenceTerminal<>(sequence);
masterSequence.add(terminal);
} | java | void add(S sequence) {
for (I item : sequence) {
masterSequence.add(item);
}
SequenceTerminal<S> terminal = new SequenceTerminal<>(sequence);
masterSequence.add(terminal);
} | [
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545 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/Sequence.java | Sequence.iterator | @Override
public Iterator<Object> iterator() {
return new Iterator<Object>() {
int currentPosition = 0;
@Override
public boolean hasNext() {
return masterSequence.size() > currentPosition;
}
@Override
public Object ne... | java | @Override
public Iterator<Object> iterator() {
return new Iterator<Object>() {
int currentPosition = 0;
@Override
public boolean hasNext() {
return masterSequence.size() > currentPosition;
}
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public Object ne... | [
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546 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/Edge.java | Edge.insert | void insert(Suffix<T, S> suffix, ActivePoint<T, S> activePoint) {
Object item = suffix.getEndItem();
Object nextItem = getItemAt(activePoint.getLength());
if (item.equals(nextItem)) {
activePoint.incrementLength();
} else {
split(suffix, activePoint);
... | java | void insert(Suffix<T, S> suffix, ActivePoint<T, S> activePoint) {
Object item = suffix.getEndItem();
Object nextItem = getItemAt(activePoint.getLength());
if (item.equals(nextItem)) {
activePoint.incrementLength();
} else {
split(suffix, activePoint);
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547 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/Edge.java | Edge.split | private void split(Suffix<T, S> suffix, ActivePoint<T, S> activePoint) {
Node<T, S> breakNode = new Node<>(this, sequence, tree);
Edge<T, S> newEdge = new Edge<>(suffix.getEndPosition() - 1, breakNode,
sequence, tree);
breakNode.insert(newEdge);
Edge<T, S> oldEdge = new E... | java | private void split(Suffix<T, S> suffix, ActivePoint<T, S> activePoint) {
Node<T, S> breakNode = new Node<>(this, sequence, tree);
Edge<T, S> newEdge = new Edge<>(suffix.getEndPosition() - 1, breakNode,
sequence, tree);
breakNode.insert(newEdge);
Edge<T, S> oldEdge = new E... | [
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548 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/Edge.java | Edge.getItemAt | @SuppressWarnings("unchecked")
T getItemAt(int position) {
if (position > getLength())
throw new IllegalArgumentException("Index " + position
+ " is greater than " + getLength()
+ " - the length of this edge.");
return (T) sequence.getItem(start + position... | java | @SuppressWarnings("unchecked")
T getItemAt(int position) {
if (position > getLength())
throw new IllegalArgumentException("Index " + position
+ " is greater than " + getLength()
+ " - the length of this edge.");
return (T) sequence.getItem(start + position... | [
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549 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/Edge.java | Edge.iterator | public Iterator<T> iterator() {
return new Iterator<T>() {
private int currentPosition = start;
private boolean hasNext = true;
public boolean hasNext() {
return hasNext;
}
@SuppressWarnings("unchecked")
public T next() {
... | java | public Iterator<T> iterator() {
return new Iterator<T>() {
private int currentPosition = start;
private boolean hasNext = true;
public boolean hasNext() {
return hasNext;
}
@SuppressWarnings("unchecked")
public T next() {
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550 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/dekker/island/Island.java | Island.isCompetitor | public boolean isCompetitor(Island isl) {
for (Coordinate c : isl) {
for (Coordinate d : islandCoordinates) {
if (c.sameColumn(d) || c.sameRow(d)) return true;
}
}
return false;
} | java | public boolean isCompetitor(Island isl) {
for (Coordinate c : isl) {
for (Coordinate d : islandCoordinates) {
if (c.sameColumn(d) || c.sameRow(d)) return true;
}
}
return false;
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551 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/dekker/token_index/Block.java | Block.getAllOccurrencesAsRanges | public IntStream getAllOccurrencesAsRanges() {
IntStream result = IntStream.empty();
// with/or without end
for (int i = start; i < end; i++) {
// every i is one occurrence
int token_position = tokenIndex.suffix_array[i];
IntStream range = IntStream.range(toke... | java | public IntStream getAllOccurrencesAsRanges() {
IntStream result = IntStream.empty();
// with/or without end
for (int i = start; i < end; i++) {
// every i is one occurrence
int token_position = tokenIndex.suffix_array[i];
IntStream range = IntStream.range(toke... | [
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552 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/QSufSort.java | QSufSort.select_sort_split | private void select_sort_split(int p, int n) {
int pa, pb, pi, pn;
int f, v;
pa = p; /* pa is start of group being picked out. */
pn = p + n - 1; /* pn is last position of subarray. */
while (pa < pn) {
for (pi = pb = pa + 1, f = KEY(pa); pi <= pn; ++pi)
... | java | private void select_sort_split(int p, int n) {
int pa, pb, pi, pn;
int f, v;
pa = p; /* pa is start of group being picked out. */
pn = p + n - 1; /* pn is last position of subarray. */
while (pa < pn) {
for (pi = pb = pa + 1, f = KEY(pa); pi <= pn; ++pi)
... | [
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553 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/SuffixArrays.java | SuffixArrays.createWithLCP | public static SuffixData createWithLCP(CharSequence s, ISuffixArrayBuilder builder) {
final CharSequenceAdapter adapter = new CharSequenceAdapter(builder);
final int[] sa = adapter.buildSuffixArray(s);
final int[] lcp = computeLCP(adapter.input, 0, s.length(), sa);
return new SuffixData(... | java | public static SuffixData createWithLCP(CharSequence s, ISuffixArrayBuilder builder) {
final CharSequenceAdapter adapter = new CharSequenceAdapter(builder);
final int[] sa = adapter.buildSuffixArray(s);
final int[] lcp = computeLCP(adapter.input, 0, s.length(), sa);
return new SuffixData(... | [
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554 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/SuffixArrays.java | SuffixArrays.createWithLCP | public static SuffixData createWithLCP(int[] input, int start, int length) {
final ISuffixArrayBuilder builder = new DensePositiveDecorator(
new ExtraTrailingCellsDecorator(defaultAlgorithm(), 3));
return createWithLCP(input, start, length, builder);
} | java | public static SuffixData createWithLCP(int[] input, int start, int length) {
final ISuffixArrayBuilder builder = new DensePositiveDecorator(
new ExtraTrailingCellsDecorator(defaultAlgorithm(), 3));
return createWithLCP(input, start, length, builder);
} | [
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555 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/SuffixArrays.java | SuffixArrays.createWithLCP | public static SuffixData createWithLCP(int[] input, int start, int length,
ISuffixArrayBuilder builder) {
final int[] sa = builder.buildSuffixArray(input, start, length);
final int[] lcp = computeLCP(input, start, length, sa);
return new SuffixData(sa, ... | java | public static SuffixData createWithLCP(int[] input, int start, int length,
ISuffixArrayBuilder builder) {
final int[] sa = builder.buildSuffixArray(input, start, length);
final int[] lcp = computeLCP(input, start, length, sa);
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556 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/SuffixArrays.java | SuffixArrays.createWithLCP | public static <T> SuffixData createWithLCP(T[] input, ISuffixArrayBuilder builder, Comparator<? super T> comparator) {
final GenericArrayAdapter adapter = new GenericArrayAdapter(builder, comparator);
final int[] sa = adapter.buildSuffixArray(input);
final int[] lcp = computeLCP(adapter.input, 0... | java | public static <T> SuffixData createWithLCP(T[] input, ISuffixArrayBuilder builder, Comparator<? super T> comparator) {
final GenericArrayAdapter adapter = new GenericArrayAdapter(builder, comparator);
final int[] sa = adapter.buildSuffixArray(input);
final int[] lcp = computeLCP(adapter.input, 0... | [
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557 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/Tools.java | Tools.max | static int max(int[] input, int start, int length) {
assert length >= 1;
int max = input[start];
for (int i = length - 2, index = start + 1; i >= 0; i--, index++) {
final int v = input[index];
if (v > max) {
max = v;
}
}
retur... | java | static int max(int[] input, int start, int length) {
assert length >= 1;
int max = input[start];
for (int i = length - 2, index = start + 1; i >= 0; i--, index++) {
final int v = input[index];
if (v > max) {
max = v;
}
}
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558 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/Tools.java | Tools.min | static int min(int[] input, int start, int length) {
assert length >= 1;
int min = input[start];
for (int i = length - 2, index = start + 1; i >= 0; i--, index++) {
final int v = input[index];
if (v < min) {
min = v;
}
}
retur... | java | static int min(int[] input, int start, int length) {
assert length >= 1;
int min = input[start];
for (int i = length - 2, index = start + 1; i >= 0; i--, index++) {
final int v = input[index];
if (v < min) {
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559 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/Tools.java | Tools.minmax | static MinMax minmax(int[] input, final int start, final int length) {
int max = input[start];
int min = max;
for (int i = length - 2, index = start + 1; i >= 0; i--, index++) {
final int v = input[index];
if (v > max) {
max = v;
}
... | java | static MinMax minmax(int[] input, final int start, final int length) {
int max = input[start];
int min = max;
for (int i = length - 2, index = start + 1; i >= 0; i--, index++) {
final int v = input[index];
if (v > max) {
max = v;
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560 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/Suffix.java | Suffix.getItemXFromEnd | public Object getItemXFromEnd(int distanceFromEnd) {
if ((end - (distanceFromEnd)) < start) {
throw new IllegalArgumentException(distanceFromEnd
+ " extends before the start of this suffix: ");
}
return sequence.getItem(end - distanceFromEnd);
} | java | public Object getItemXFromEnd(int distanceFromEnd) {
if ((end - (distanceFromEnd)) < start) {
throw new IllegalArgumentException(distanceFromEnd
+ " extends before the start of this suffix: ");
}
return sequence.getItem(end - distanceFromEnd);
} | [
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561 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/dekker/legacy/MatchTableSerializer.java | MatchTableSerializer.toHtml | public String toHtml(Archipelago arch) {
int mat[] = new int[rowNum()];
for (Island isl : arch.getIslands()) {
for (Coordinate c : isl) {
mat[c.row] = c.column;
}
}
StringBuilder result = new StringBuilder("<table>\n<tr><td></td>\n");
Array... | java | public String toHtml(Archipelago arch) {
int mat[] = new int[rowNum()];
for (Island isl : arch.getIslands()) {
for (Coordinate c : isl) {
mat[c.row] = c.column;
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562 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/Node.java | Node.insert | @SuppressWarnings("unchecked")
void insert(Suffix<T, S> suffix, ActivePoint<T, S> activePoint) {
Object item = suffix.getEndItem();
if (edges.containsKey(item)) {
if (tree.isNotFirstInsert() && activePoint.getNode() != tree.getRoot())
tree.setSuffixLink(activePoint.getNo... | java | @SuppressWarnings("unchecked")
void insert(Suffix<T, S> suffix, ActivePoint<T, S> activePoint) {
Object item = suffix.getEndItem();
if (edges.containsKey(item)) {
if (tree.isNotFirstInsert() && activePoint.getNode() != tree.getRoot())
tree.setSuffixLink(activePoint.getNo... | [
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563 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/Node.java | Node.insert | void insert(Edge<T, S> edge) {
if (edges.containsKey(edge.getStartItem()))
throw new IllegalArgumentException("Item " + edge.getStartItem()
+ " already exists in node " + toString());
edges.put(edge.getStartItem(), edge);
} | java | void insert(Edge<T, S> edge) {
if (edges.containsKey(edge.getStartItem()))
throw new IllegalArgumentException("Item " + edge.getStartItem()
+ " already exists in node " + toString());
edges.put(edge.getStartItem(), edge);
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564 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/Utils.java | Utils.addTerminalToSequence | static <I, S extends Iterable<I>> Object[] addTerminalToSequence(S sequence,
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ArrayList<Object> list = new ArrayList<>();
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SequenceTerminal<S> terminatingObject) {
ArrayList<Object> list = new ArrayList<>();
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565 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/Utils.java | Utils.printTreeForGraphViz | static <T, S extends Iterable<T>> String printTreeForGraphViz(SuffixTree<T, S> tree, boolean printSuffixLinks) {
LinkedList<Node<T, S>> stack = new LinkedList<>();
stack.add(tree.getRoot());
Map<Node<T, S>, Integer> nodeMap = new HashMap<>();
nodeMap.put(tree.getRoot(), 0);
int n... | java | static <T, S extends Iterable<T>> String printTreeForGraphViz(SuffixTree<T, S> tree, boolean printSuffixLinks) {
LinkedList<Node<T, S>> stack = new LinkedList<>();
stack.add(tree.getRoot());
Map<Node<T, S>, Integer> nodeMap = new HashMap<>();
nodeMap.put(tree.getRoot(), 0);
int n... | [
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566 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/CharSequenceAdapter.java | CharSequenceAdapter.buildSuffixArray | public int[] buildSuffixArray(CharSequence sequence) {
/*
* Allocate slightly more space, some suffix construction strategies need it and
* we don't want to waste space for multiple symbol mappings.
*/
this.input = new int[sequence.length() + SuffixArrays.MAX_EXTRA_TRAILING_S... | java | public int[] buildSuffixArray(CharSequence sequence) {
/*
* Allocate slightly more space, some suffix construction strategies need it and
* we don't want to waste space for multiple symbol mappings.
*/
this.input = new int[sequence.length() + SuffixArrays.MAX_EXTRA_TRAILING_S... | [
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567 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/ActivePoint.java | ActivePoint.setPosition | void setPosition(Node<T, S> node, Edge<T, S> edge, int length) {
activeNode = node;
activeEdge = edge;
activeLength = length;
} | java | void setPosition(Node<T, S> node, Edge<T, S> edge, int length) {
activeNode = node;
activeEdge = edge;
activeLength = length;
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568 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/ActivePoint.java | ActivePoint.updateAfterInsert | public void updateAfterInsert(Suffix<T, S> suffix) {
if (activeNode == root && suffix.isEmpty()) {
activeNode = root;
activeEdge = null;
activeLength = 0;
} else if (activeNode == root) {
Object item = suffix.getStart();
activeEdge = root.getEd... | java | public void updateAfterInsert(Suffix<T, S> suffix) {
if (activeNode == root && suffix.isEmpty()) {
activeNode = root;
activeEdge = null;
activeLength = 0;
} else if (activeNode == root) {
Object item = suffix.getStart();
activeEdge = root.getEd... | [
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569 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/ActivePoint.java | ActivePoint.fixActiveEdgeAfterSuffixLink | private void fixActiveEdgeAfterSuffixLink(Suffix<T, S> suffix) {
while (activeEdge != null && activeLength > activeEdge.getLength()) {
activeLength = activeLength - activeEdge.getLength();
activeNode = activeEdge.getTerminal();
Object item = suffix.getItemXFromEnd(activeLengt... | java | private void fixActiveEdgeAfterSuffixLink(Suffix<T, S> suffix) {
while (activeEdge != null && activeLength > activeEdge.getLength()) {
activeLength = activeLength - activeEdge.getLength();
activeNode = activeEdge.getTerminal();
Object item = suffix.getItemXFromEnd(activeLengt... | [
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570 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/ActivePoint.java | ActivePoint.findTrueActiveEdge | private void findTrueActiveEdge() {
if (activeEdge != null) {
Object item = activeEdge.getStartItem();
activeEdge = activeNode.getEdgeStarting(item);
}
} | java | private void findTrueActiveEdge() {
if (activeEdge != null) {
Object item = activeEdge.getStartItem();
activeEdge = activeNode.getEdgeStarting(item);
}
} | [
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571 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/ActivePoint.java | ActivePoint.resetActivePointToTerminal | private boolean resetActivePointToTerminal() {
if (activeEdge != null && activeEdge.getLength() == activeLength && activeEdge.isTerminating()) {
activeNode = activeEdge.getTerminal();
activeEdge = null;
activeLength = 0;
return true;
}
return false... | java | private boolean resetActivePointToTerminal() {
if (activeEdge != null && activeEdge.getLength() == activeLength && activeEdge.isTerminating()) {
activeNode = activeEdge.getTerminal();
activeEdge = null;
activeLength = 0;
return true;
}
return false... | [
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572 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixarray/GenericArrayAdapter.java | GenericArrayAdapter.buildSuffixArray | public int[] buildSuffixArray(T[] tokens) {
final int length = tokens.length;
/*
* Allocate slightly more space, some suffix construction strategies need it and
* we don't want to waste space for multiple symbol mappings.
*/
input = new int[length + SuffixArrays.MAX_EX... | java | public int[] buildSuffixArray(T[] tokens) {
final int length = tokens.length;
/*
* Allocate slightly more space, some suffix construction strategies need it and
* we don't want to waste space for multiple symbol mappings.
*/
input = new int[length + SuffixArrays.MAX_EX... | [
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573 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/SuffixTree.java | SuffixTree.add | public void add(S sequence) {
int start = currentEnd;
this.sequence.add(sequence);
suffix = new Suffix<>(currentEnd, currentEnd, this.sequence);
activePoint.setPosition(root, null, 0);
extendTree(start, this.sequence.getLength());
} | java | public void add(S sequence) {
int start = currentEnd;
this.sequence.add(sequence);
suffix = new Suffix<>(currentEnd, currentEnd, this.sequence);
activePoint.setPosition(root, null, 0);
extendTree(start, this.sequence.getLength());
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574 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/SuffixTree.java | SuffixTree.insert | void insert(Suffix<I, S> suffix) {
if (activePoint.isNode()) {
Node<I, S> node = activePoint.getNode();
node.insert(suffix, activePoint);
} else if (activePoint.isEdge()) {
Edge<I, S> edge = activePoint.getEdge();
edge.insert(suffix, activePoint);
... | java | void insert(Suffix<I, S> suffix) {
if (activePoint.isNode()) {
Node<I, S> node = activePoint.getNode();
node.insert(suffix, activePoint);
} else if (activePoint.isEdge()) {
Edge<I, S> edge = activePoint.getEdge();
edge.insert(suffix, activePoint);
... | [
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575 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/suffixtree/SuffixTree.java | SuffixTree.setSuffixLink | void setSuffixLink(Node<I, S> node) {
if (isNotFirstInsert()) {
lastNodeInserted.setSuffixLink(node);
}
lastNodeInserted = node;
} | java | void setSuffixLink(Node<I, S> node) {
if (isNotFirstInsert()) {
lastNodeInserted.setSuffixLink(node);
}
lastNodeInserted = node;
} | [
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node. This method checks the state of the step and only applies the
suffix link if there is a previous node inserted during this step. This
method also set the last node inserted to the supplied node after
applying any suffix linking.
@param node ... | [
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576 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/dekker/legacy/MatchTableImpl.java | MatchTableImpl.create | public static MatchTable create(VariantGraph graph, Iterable<Token> witness) {
Comparator<Token> comparator = new EqualityTokenComparator();
return MatchTableImpl.create(graph, witness, comparator);
} | java | public static MatchTable create(VariantGraph graph, Iterable<Token> witness) {
Comparator<Token> comparator = new EqualityTokenComparator();
return MatchTableImpl.create(graph, witness, comparator);
} | [
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577 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/dekker/legacy/MatchTableImpl.java | MatchTableImpl.getIslands | @Override
public Set<Island> getIslands() {
Map<Coordinate, Island> coordinateMapper = new HashMap<>();
List<Coordinate> allMatches = allMatches();
for (Coordinate c : allMatches) {
// LOG.debug("coordinate {}", c);
addToIslands(coordinateMapper, c);
}
... | java | @Override
public Set<Island> getIslands() {
Map<Coordinate, Island> coordinateMapper = new HashMap<>();
List<Coordinate> allMatches = allMatches();
for (Coordinate c : allMatches) {
// LOG.debug("coordinate {}", c);
addToIslands(coordinateMapper, c);
}
... | [
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578 | interedition/collatex | collatex-core/src/main/java/eu/interedition/collatex/dekker/legacy/MatchTableImpl.java | MatchTableImpl.fillTableWithMatches | private void fillTableWithMatches(VariantGraphRanking ranking, VariantGraph graph, Iterable<Token> witness, Comparator<Token> comparator) {
Matches matches = Matches.between(graph.vertices(), witness, comparator);
Set<Token> unique = matches.uniqueInWitness;
Set<Token> ambiguous = matches.ambigu... | java | private void fillTableWithMatches(VariantGraphRanking ranking, VariantGraph graph, Iterable<Token> witness, Comparator<Token> comparator) {
Matches matches = Matches.between(graph.vertices(), witness, comparator);
Set<Token> unique = matches.uniqueInWitness;
Set<Token> ambiguous = matches.ambigu... | [
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579 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/MutableSymbolTable.java | MutableSymbolTable.remove | public void remove(int id) {
String symbol = invert().keyForId(id);
idToSymbol.remove(id);
symbolToId.remove(symbol);
} | java | public void remove(int id) {
String symbol = invert().keyForId(id);
idToSymbol.remove(id);
symbolToId.remove(symbol);
} | [
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@see #trimIds() for a way to compact the assigned ids
@param id | [
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580 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/MutableSymbolTable.java | MutableSymbolTable.trimIds | public void trimIds() {
// typical case shortcut
if (idToSymbol.containsKey(nextId - 1)) {
return;
}
int max = -1;
for (IntObjectCursor<String> cursor : idToSymbol) {
max = Math.max(max, cursor.key);
}
nextId = max + 1;
} | java | public void trimIds() {
// typical case shortcut
if (idToSymbol.containsKey(nextId - 1)) {
return;
}
int max = -1;
for (IntObjectCursor<String> cursor : idToSymbol) {
max = Math.max(max, cursor.key);
}
nextId = max + 1;
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581 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/operations/Compose.java | Compose.precomputeInner | public static PrecomputedComposeFst precomputeInner(Fst fst2, Semiring semiring) {
fst2.throwIfInvalid();
MutableFst mutableFst = MutableFst.copyFrom(fst2);
WriteableSymbolTable table = mutableFst.getInputSymbols();
int e1index = getOrAddEps(table, true);
int e2index = getOrAddEps(table, false);
... | java | public static PrecomputedComposeFst precomputeInner(Fst fst2, Semiring semiring) {
fst2.throwIfInvalid();
MutableFst mutableFst = MutableFst.copyFrom(fst2);
WriteableSymbolTable table = mutableFst.getInputSymbols();
int e1index = getOrAddEps(table, true);
int e2index = getOrAddEps(table, false);
... | [
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@return a pre-processed form of the inner fst that can be passed to `composeWithPrecom... | [
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582 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/operations/Compose.java | Compose.makeFilter | private static MutableFst makeFilter(WriteableSymbolTable table, Semiring semiring, String eps1, String eps2) {
MutableFst filter = new MutableFst(semiring, table, table);
// State 0
MutableState s0 = filter.newStartState();
s0.setFinalWeight(semiring.one());
MutableState s1 = filter.newState();
... | java | private static MutableFst makeFilter(WriteableSymbolTable table, Semiring semiring, String eps1, String eps2) {
MutableFst filter = new MutableFst(semiring, table, table);
// State 0
MutableState s0 = filter.newStartState();
s0.setFinalWeight(semiring.one());
MutableState s1 = filter.newState();
... | [
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@param table the filter's input/output symbols
@param semiring the semiring to use in the operation | [
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] | 4c675203015c1cfad2072556cb532b6edc73261d | https://github.com/steveash/jopenfst/blob/4c675203015c1cfad2072556cb532b6edc73261d/src/main/java/com/github/steveash/jopenfst/operations/Compose.java#L190-L219 |
583 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/operations/Compose.java | Compose.augment | private static void augment(AugmentLabels label, MutableFst fst, Semiring semiring, String eps1, String eps2) {
// label: 0->augment on ilabel
// 1->augment on olabel
int e1inputIndex = fst.getInputSymbols().getOrAdd(eps1);
int e2inputIndex = fst.getInputSymbols().getOrAdd(eps2);
int e1outputIndex... | java | private static void augment(AugmentLabels label, MutableFst fst, Semiring semiring, String eps1, String eps2) {
// label: 0->augment on ilabel
// 1->augment on olabel
int e1inputIndex = fst.getInputSymbols().getOrAdd(eps1);
int e2inputIndex = fst.getInputSymbols().getOrAdd(eps2);
int e1outputIndex... | [
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@param label constant denoting if the augment should take place on input or output labels For value equal to 0
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584 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/operations/Project.java | Project.apply | public static void apply(MutableFst fst, ProjectType pType) {
if (pType == ProjectType.INPUT) {
fst.setOutputSymbolsAsCopyFromThatInput(fst);
} else if (pType == ProjectType.OUTPUT) {
fst.setInputSymbolsAsCopyFromThatOutput(fst);
}
for (int i = 0; i < fst.getStateCount(); i++) {
Mutab... | java | public static void apply(MutableFst fst, ProjectType pType) {
if (pType == ProjectType.INPUT) {
fst.setOutputSymbolsAsCopyFromThatInput(fst);
} else if (pType == ProjectType.OUTPUT) {
fst.setInputSymbolsAsCopyFromThatOutput(fst);
}
for (int i = 0; i < fst.getStateCount(); i++) {
Mutab... | [
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585 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/operations/Connect.java | Connect.apply | public static void apply(MutableFst fst) {
fst.throwIfInvalid();
IntOpenHashSet accessible = new IntOpenHashSet(fst.getStateCount());
IntOpenHashSet coaccessible = new IntOpenHashSet(fst.getStateCount());
dfsForward(fst.getStartState(), accessible);
int numStates = fst.getStateCount();
for (int... | java | public static void apply(MutableFst fst) {
fst.throwIfInvalid();
IntOpenHashSet accessible = new IntOpenHashSet(fst.getStateCount());
IntOpenHashSet coaccessible = new IntOpenHashSet(fst.getStateCount());
dfsForward(fst.getStartState(), accessible);
int numStates = fst.getStateCount();
for (int... | [
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586 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/MutableFst.java | MutableFst.setStart | public MutableState setStart(MutableState start) {
checkArgument(start.getId() >= 0, "must set id before setting start");
throwIfSymbolTableMissingId(start.getId());
correctStateWeight(start);
this.start = start;
return start;
} | java | public MutableState setStart(MutableState start) {
checkArgument(start.getId() >= 0, "must set id before setting start");
throwIfSymbolTableMissingId(start.getId());
correctStateWeight(start);
this.start = start;
return start;
} | [
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587 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/MutableFst.java | MutableFst.deleteStates | public void deleteStates(Collection<MutableState> statesToDelete) {
if (statesToDelete.isEmpty()) {
return;
}
for (MutableState state : statesToDelete) {
deleteState(state);
}
remapStateIds();
} | java | public void deleteStates(Collection<MutableState> statesToDelete) {
if (statesToDelete.isEmpty()) {
return;
}
for (MutableState state : statesToDelete) {
deleteState(state);
}
remapStateIds();
} | [
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588 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/MutableFst.java | MutableFst.deleteState | private void deleteState(MutableState state) {
if (state.getId() == this.start.getId()) {
throw new IllegalArgumentException("Cannot delete start state.");
}
// we're going to "compact" all of the nulls out and remap state ids at the end
this.states.set(state.getId(), null);
if (isUsingStateSy... | java | private void deleteState(MutableState state) {
if (state.getId() == this.start.getId()) {
throw new IllegalArgumentException("Cannot delete start state.");
}
// we're going to "compact" all of the nulls out and remap state ids at the end
this.states.set(state.getId(), null);
if (isUsingStateSy... | [
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589 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/operations/Determinize.java | Determinize.compute | public MutableFst compute(final Fst fst) {
fst.throwIfInvalid();
// init for this run of compute
this.semiring = fst.getSemiring();
this.gallicSemiring = new GallicSemiring(this.semiring, this.gallicMode);
this.unionSemiring = makeUnionRing(semiring, gallicSemiring, mode);
this.inputFst = fst;
... | java | public MutableFst compute(final Fst fst) {
fst.throwIfInvalid();
// init for this run of compute
this.semiring = fst.getSemiring();
this.gallicSemiring = new GallicSemiring(this.semiring, this.gallicMode);
this.unionSemiring = makeUnionRing(semiring, gallicSemiring, mode);
this.inputFst = fst;
... | [
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590 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/operations/Determinize.java | Determinize.normalizeArcWork | private void normalizeArcWork(final DetArcWork arcWork) {
Collections.sort(arcWork.pendingElements);
ArrayList<DetElement> deduped = Lists.newArrayList();
for (int i = 0; i < arcWork.pendingElements.size(); i++) {
// first update the running common divisor that we'll use later
DetElement current... | java | private void normalizeArcWork(final DetArcWork arcWork) {
Collections.sort(arcWork.pendingElements);
ArrayList<DetElement> deduped = Lists.newArrayList();
for (int i = 0; i < arcWork.pendingElements.size(); i++) {
// first update the running common divisor that we'll use later
DetElement current... | [
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591 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/operations/Determinize.java | Determinize.computeFinalWeight | private double computeFinalWeight(final int outputStateId,
final DetStateTuple targetTuple,
Deque<DetElement> finalQueue) {
UnionWeight<GallicWeight> result = this.unionSemiring.zero();
for (DetElement detElement : targetTuple.getElements()... | java | private double computeFinalWeight(final int outputStateId,
final DetStateTuple targetTuple,
Deque<DetElement> finalQueue) {
UnionWeight<GallicWeight> result = this.unionSemiring.zero();
for (DetElement detElement : targetTuple.getElements()... | [
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592 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/operations/Determinize.java | Determinize.expandDeferredFinalStates | private void expandDeferredFinalStates(Deque<DetElement> finalQueue) {
HashBiMap<Integer, GallicWeight> outputStateIdToFinalSuffix = HashBiMap.create();
while (!finalQueue.isEmpty()) {
DetElement element = finalQueue.removeFirst();
for (GallicWeight gallicWeight : element.residual.getWeights()) {
... | java | private void expandDeferredFinalStates(Deque<DetElement> finalQueue) {
HashBiMap<Integer, GallicWeight> outputStateIdToFinalSuffix = HashBiMap.create();
while (!finalQueue.isEmpty()) {
DetElement element = finalQueue.removeFirst();
for (GallicWeight gallicWeight : element.residual.getWeights()) {
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593 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/FstInputOutput.java | FstInputOutput.readStringMap | public static MutableSymbolTable readStringMap(ObjectInput in)
throws IOException, ClassNotFoundException {
int mapSize = in.readInt();
MutableSymbolTable syms = new MutableSymbolTable();
for (int i = 0; i < mapSize; i++) {
String sym = in.readUTF();
int index = in.readInt();
syms.p... | java | public static MutableSymbolTable readStringMap(ObjectInput in)
throws IOException, ClassNotFoundException {
int mapSize = in.readInt();
MutableSymbolTable syms = new MutableSymbolTable();
for (int i = 0; i < mapSize; i++) {
String sym = in.readUTF();
int index = in.readInt();
syms.p... | [
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@param in the java.io.ObjectInput. It should be already be initialized by the caller.
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594 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/FstInputOutput.java | FstInputOutput.readFstFromBinaryStream | public static MutableFst readFstFromBinaryStream(ObjectInput in) throws IOException,
ClassNotFoundException {
int version = in.readInt();
if (version < FIRST_VERSION && version > CURRENT_VERSION) {
throw new IllegalArgumentException... | java | public static MutableFst readFstFromBinaryStream(ObjectInput in) throws IOException,
ClassNotFoundException {
int version = in.readInt();
if (version < FIRST_VERSION && version > CURRENT_VERSION) {
throw new IllegalArgumentException... | [
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595 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/FstInputOutput.java | FstInputOutput.writeStringMap | private static void writeStringMap(SymbolTable map, ObjectOutput out)
throws IOException {
out.writeInt(map.size());
for (ObjectIntCursor<String> cursor : map) {
out.writeUTF(cursor.key);
out.writeInt(cursor.value);
}
} | java | private static void writeStringMap(SymbolTable map, ObjectOutput out)
throws IOException {
out.writeInt(map.size());
for (ObjectIntCursor<String> cursor : map) {
out.writeUTF(cursor.key);
out.writeInt(cursor.value);
}
} | [
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596 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/FstInputOutput.java | FstInputOutput.writeFstToBinaryStream | public static void writeFstToBinaryStream(Fst fst, ObjectOutput out) throws IOException {
out.writeInt(CURRENT_VERSION);
writeStringMap(fst.getInputSymbols(), out);
writeStringMap(fst.getOutputSymbols(), out);
out.writeBoolean(fst.isUsingStateSymbols()); // whether or not we used a state symbol table
... | java | public static void writeFstToBinaryStream(Fst fst, ObjectOutput out) throws IOException {
out.writeInt(CURRENT_VERSION);
writeStringMap(fst.getInputSymbols(), out);
writeStringMap(fst.getOutputSymbols(), out);
out.writeBoolean(fst.isUsingStateSymbols()); // whether or not we used a state symbol table
... | [
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597 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/operations/ArcSort.java | ArcSort.sortBy | public static void sortBy(MutableFst fst, Comparator<Arc> comparator) {
int numStates = fst.getStateCount();
for (int i = 0; i < numStates; i++) {
MutableState s = fst.getState(i);
s.arcSort(comparator);
}
} | java | public static void sortBy(MutableFst fst, Comparator<Arc> comparator) {
int numStates = fst.getStateCount();
for (int i = 0; i < numStates; i++) {
MutableState s = fst.getState(i);
s.arcSort(comparator);
}
} | [
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"numStat... | Applies the ArcSort on the provided fst. Sorting can be applied either on input or output label based on the
provided comparator.
@param fst the fst to sort it's arcs
@param comparator the provided Comparator | [
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] | 4c675203015c1cfad2072556cb532b6edc73261d | https://github.com/steveash/jopenfst/blob/4c675203015c1cfad2072556cb532b6edc73261d/src/main/java/com/github/steveash/jopenfst/operations/ArcSort.java#L59-L65 |
598 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/operations/ArcSort.java | ArcSort.isSorted | public static boolean isSorted(State state, Comparator<Arc> comparator) {
return Ordering.from(comparator).isOrdered(state.getArcs());
} | java | public static boolean isSorted(State state, Comparator<Arc> comparator) {
return Ordering.from(comparator).isOrdered(state.getArcs());
} | [
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@return | [
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] | 4c675203015c1cfad2072556cb532b6edc73261d | https://github.com/steveash/jopenfst/blob/4c675203015c1cfad2072556cb532b6edc73261d/src/main/java/com/github/steveash/jopenfst/operations/ArcSort.java#L73-L75 |
599 | steveash/jopenfst | src/main/java/com/github/steveash/jopenfst/io/Convert.java | Convert.exportFst | private static void exportFst(Fst fst, String filename) {
FileWriter file;
try {
file = new FileWriter(filename);
PrintWriter out = new PrintWriter(file);
// print start first
State start = fst.getStartState();
out.println(start.getId() + "\t" + start.getFinalWeight());
// ... | java | private static void exportFst(Fst fst, String filename) {
FileWriter file;
try {
file = new FileWriter(filename);
PrintWriter out = new PrintWriter(file);
// print start first
State start = fst.getStartState();
out.println(start.getId() + "\t" + start.getFinalWeight());
// ... | [
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@param fst the fst to export
@param filename the openfst's fst.txt filename | [
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] | 4c675203015c1cfad2072556cb532b6edc73261d | https://github.com/steveash/jopenfst/blob/4c675203015c1cfad2072556cb532b6edc73261d/src/main/java/com/github/steveash/jopenfst/io/Convert.java#L156-L207 |
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